Locus 11714

Sequence ID dm3.chr3R
Location 23,288,654 – 23,288,790
Length 136
Max. P 0.962474
window16090 window16091 window16092 window16093

overview

Window 0

Location 23,288,654 – 23,288,762
Length 108
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 73.41
Shannon entropy 0.52119
G+C content 0.47645
Mean single sequence MFE -32.91
Consensus MFE -15.90
Energy contribution -16.75
Covariance contribution 0.85
Combinations/Pair 1.11
Mean z-score -1.48
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.715566
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23288654 108 + 27905053
AUUUGGCAUUUUAUUCGCUUCCUGGUGAUGGUGAUGAUAAUGGUGCUGCUGCU---CCAAGUGCCGGUCAG-UGUGGCAACAAAUGUUGCCAAAGGCUGUGCCACAAUUCGU
....((((((....(((((..(....)..)))))......(((.((....)).---)))))))))((((((-(.(((((((....)))))))...)))).)))......... ( -37.40, z-score =  -1.68, R)
>droSim1.chr3R 23025278 107 + 27517382
AUUUGGCAUUUUAUUCGCUUCCUGGUAAUGGUGAUGAUGAUGCUGCUGCUGCUGCUCCAAGUGCCGGUCAG-UGUGGCA--CAAUGUUGCCAAAGGCUGUGC-ACA-UUCGU
....((((((....(((((..........)))))....))))))(..((....))..)..(((((((((..-..(((((--......)))))..))))).))-)).-..... ( -31.70, z-score =   0.63, R)
>droYak2.chr3R 5628965 94 - 28832112
AUUUGGCAUUUUAUUCGCAUCCUGGUGAUGAUGAUGCU------------------CCAAGUGCCGGUCAUCUGUGGCAACAAAUGUUGCCAAAUCCAGUGCCACAAUUCGU
....(((((((.....(((((...........))))).------------------..)))))))((.((.((((((((((....)))))))....)))))))......... ( -28.30, z-score =  -1.43, R)
>droEre2.scaffold_4820 5727263 104 - 10470090
AUUUGGCAUUUUAUUCGCUGCCCGGUGAUGCC-AUCGUCAUGCUGCUGCUG------CAAGUGCCGGUCAG-UGUGGCAACAAAUGUUGCCAAAUGCUGUGCCACAAUUCGU
...((((((..(((((((((.(((((((((..-..))))..(((((....)------).)))))))).)))-))(((((((....)))))))))))..))))))........ ( -40.50, z-score =  -2.31, R)
>droAna3.scaffold_13340 4309180 107 - 23697760
AUUUGGCAUUUUAUUCGUUUCCUGACC-CGGCACGGCUGAUGAUGCUGAUACUUUCCCAA---CUGGUCAG-UGUGGCAACAAAUGUUGCCAAAUGCCGAGCCACAAUUCGU
...((((.........(((....))).-(((((((((.......))))(((((..((...---..))..))-)))((((((....))))))...))))).))))........ ( -33.10, z-score =  -1.91, R)
>droWil1.scaffold_181089 3531162 89 + 12369635
AUUUGGCAUUUCAUUCGUUUCCUG------------CUGCAGUUGUUGCUACAU---------CUGGUCAA-UGUGGCAACAAAUGUUGCCAG-UUCUGUGCCACAAUUCGU
...((((((............(((------------(.(((.((((((((((((---------.......)-))))))))))).))).).)))-....))))))........ ( -26.49, z-score =  -2.17, R)
>consensus
AUUUGGCAUUUUAUUCGCUUCCUGGUGAUGGUGAUGCUGAUGCUGCUGCUGCU___CCAAGUGCCGGUCAG_UGUGGCAACAAAUGUUGCCAAAUGCUGUGCCACAAUUCGU
...((((((............(((((....................................))))).......(((((((....)))))))......))))))........ (-15.90 = -16.75 +   0.85)

alignment

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secondary structure

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dotplot

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Window 1

Location 23,288,654 – 23,288,762
Length 108
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 73.41
Shannon entropy 0.52119
G+C content 0.47645
Mean single sequence MFE -28.55
Consensus MFE -14.94
Energy contribution -15.72
Covariance contribution 0.78
Combinations/Pair 1.12
Mean z-score -1.10
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.07
SVM RNA-class probability 0.528041
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23288654 108 - 27905053
ACGAAUUGUGGCACAGCCUUUGGCAACAUUUGUUGCCACA-CUGACCGGCACUUGG---AGCAGCAGCACCAUUAUCAUCACCAUCACCAGGAAGCGAAUAAAAUGCCAAAU
........((((((((....(((((((....)))))))..-)))....((...(((---.((....)).))).........((.......))..))........)))))... ( -26.90, z-score =  -0.62, R)
>droSim1.chr3R 23025278 107 - 27517382
ACGAA-UGU-GCACAGCCUUUGGCAACAUUG--UGCCACA-CUGACCGGCACUUGGAGCAGCAGCAGCAGCAUCAUCAUCACCAUUACCAGGAAGCGAAUAAAAUGCCAAAU
.....-(((-((((((....((....)))))--)).))))-......((((..((..((.((....)).))..))......((.......))............)))).... ( -21.60, z-score =   1.56, R)
>droYak2.chr3R 5628965 94 + 28832112
ACGAAUUGUGGCACUGGAUUUGGCAACAUUUGUUGCCACAGAUGACCGGCACUUGG------------------AGCAUCAUCAUCACCAGGAUGCGAAUAAAAUGCCAAAU
........(((((((((...(((((((....)))))))..(((((...((......------------------.)).)))))....)))).((....))....)))))... ( -27.90, z-score =  -1.63, R)
>droEre2.scaffold_4820 5727263 104 + 10470090
ACGAAUUGUGGCACAGCAUUUGGCAACAUUUGUUGCCACA-CUGACCGGCACUUG------CAGCAGCAGCAUGACGAU-GGCAUCACCGGGCAGCGAAUAAAAUGCCAAAU
........(((((.......(((((((....)))))))(.-(((.((((....((------(.(((......)).)...-.)))...)))).))).).......)))))... ( -31.40, z-score =  -0.51, R)
>droAna3.scaffold_13340 4309180 107 + 23697760
ACGAAUUGUGGCUCGGCAUUUGGCAACAUUUGUUGCCACA-CUGACCAG---UUGGGAAAGUAUCAGCAUCAUCAGCCGUGCCG-GGUCAGGAAACGAAUAAAAUGCCAAAU
.((..((.(((((((((((.(((((((....)))))))..-((((...(---((((.......)))))....))))..))))))-))))).))..))............... ( -37.40, z-score =  -2.69, R)
>droWil1.scaffold_181089 3531162 89 - 12369635
ACGAAUUGUGGCACAGAA-CUGGCAACAUUUGUUGCCACA-UUGACCAG---------AUGUAGCAACAACUGCAG------------CAGGAAACGAAUGAAAUGCCAAAU
........((((((((..-.((....)).(((((((.(((-((.....)---------)))).))))))))))((.------------..(....)...))...)))))... ( -26.10, z-score =  -2.71, R)
>consensus
ACGAAUUGUGGCACAGCAUUUGGCAACAUUUGUUGCCACA_CUGACCGGCACUUGG___AGCAGCAGCAGCAUCAGCAUCACCAUCACCAGGAAGCGAAUAAAAUGCCAAAU
........((((((((....(((((((....)))))))...)))..............................................(....)........)))))... (-14.94 = -15.72 +   0.78)

alignment

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secondary structure

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dotplot

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Window 2

Location 23,288,693 – 23,288,790
Length 97
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 69.99
Shannon entropy 0.54490
G+C content 0.50633
Mean single sequence MFE -30.62
Consensus MFE -14.16
Energy contribution -15.38
Covariance contribution 1.22
Combinations/Pair 1.06
Mean z-score -1.29
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.563398
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23288693 97 + 27905053
---AUGGUGCUGCUGCUCCAAGUGCCGGUCAG-UGUGGCAACAAAUGUUGCCAAAGGCUGUGCCACAAUUCGUUUCAUUUGCGGCCAACGGGAACGGGAAC------
---.(((.((....)).))).(((((((((..-..(((((((....)))))))..))))).).)))..((((((((..(((....)))..))))))))...------ ( -33.80, z-score =  -0.38, R)
>droSim1.chr3R 23025317 93 + 27517382
AUGCUGCUGCUGCUGCUCCAAGUGCCGGUCAG-UGUGGCAC--AAUGUUGCCAAAGGCUGUGC-ACA-UUCGUUUCAUUUGCGGCC-ACGGAACGGAAC--------
..((.((....)).)).....(((((((((..-..(((((.--.....)))))..))))).))-)).-((((((((..........-..))))))))..-------- ( -30.20, z-score =   0.65, R)
>droYak2.chr3R 5628992 88 - 28832112
------AUGAUGAUGCUCCAAGUGCCGGUCAUCUGUGGCAACAAAUGUUGCCAAAUCCAGUGCCACAAUUCGUUUCAUUUGCGGCAAACGGCAG-------------
------................(((((.....((((((((((....)))))))....)))((((.(((..........))).))))..))))).------------- ( -27.20, z-score =  -1.33, R)
>droEre2.scaffold_4820 5727301 84 - 10470090
------AUGCUGCUGCUGCAAGUGCCGGUCAG-UGUGGCAACAAAUGUUGCCAAAUGCUGUGCCACAAUUCGUUUCAUUUGCGGCCCACGG----------------
------...(((..((((((((((..((((((-(.(((((((....)))))))...)))).)))((.....))..))))))))))...)))---------------- ( -32.10, z-score =  -1.51, R)
>droAna3.scaffold_13340 4309218 85 - 23697760
---AUGAUGCUGAUACUUUCCCAACUGGUCAG-UGUGGCAACAAAUGUUGCCAAAUGCCGAGCCACAAUUCGUUUAAUUUGCGGCCACC------------------
---...((((((((.............)))))-)))((((((....)))))).......(.(((.(((..........))).))))...------------------ ( -22.02, z-score =  -0.87, R)
>droWil1.scaffold_181089 3531189 96 + 12369635
---------CAGUUGUUGCUACAUCUGGUCAA-UGUGGCAACAAAUGUUGCCAG-UUCUGUGCCACAAUUCGUUUAAUUUGUGGCUAGAGCACAUUGAGAAGUGGAC
---------(((.(((....))).))).((((-(((((((((....)))))).(-(((((.(((((((..........))))))))))))))))))))......... ( -38.40, z-score =  -4.29, R)
>consensus
______AUGCUGCUGCUCCAAGUGCCGGUCAG_UGUGGCAACAAAUGUUGCCAAAUGCUGUGCCACAAUUCGUUUCAUUUGCGGCCAACGG_A______________
........................(((........(((((((....)))))))........(((.(((..........))).)))...)))................ (-14.16 = -15.38 +   1.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 23,288,693 – 23,288,790
Length 97
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 69.99
Shannon entropy 0.54490
G+C content 0.50633
Mean single sequence MFE -29.12
Consensus MFE -18.53
Energy contribution -19.40
Covariance contribution 0.87
Combinations/Pair 1.33
Mean z-score -1.39
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.71
SVM RNA-class probability 0.962474
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23288693 97 - 27905053
------GUUCCCGUUCCCGUUGGCCGCAAAUGAAACGAAUUGUGGCACAGCCUUUGGCAACAUUUGUUGCCACA-CUGACCGGCACUUGGAGCAGCAGCACCAU---
------(((((.((.((.(((((((((((..........))))))).))))...(((((((....)))))))..-......)).))..)))))...........--- ( -32.80, z-score =  -1.40, R)
>droSim1.chr3R 23025317 93 - 27517382
--------GUUCCGUUCCGU-GGCCGCAAAUGAAACGAA-UGU-GCACAGCCUUUGGCAACAUU--GUGCCACA-CUGACCGGCACUUGGAGCAGCAGCAGCAGCAU
--------(((((((((((.-(((.(((.((.......)-).)-))...)))..))).)))...--(((((...-......)))))..))))).((....))..... ( -26.90, z-score =   0.89, R)
>droYak2.chr3R 5628992 88 + 28832112
-------------CUGCCGUUUGCCGCAAAUGAAACGAAUUGUGGCACUGGAUUUGGCAACAUUUGUUGCCACAGAUGACCGGCACUUGGAGCAUCAUCAU------
-------------.(((((..((((((((..........))))))))(((....(((((((....)))))))))).....)))))................------ ( -29.20, z-score =  -1.89, R)
>droEre2.scaffold_4820 5727301 84 + 10470090
----------------CCGUGGGCCGCAAAUGAAACGAAUUGUGGCACAGCAUUUGGCAACAUUUGUUGCCACA-CUGACCGGCACUUGCAGCAGCAGCAU------
----------------..(((((((((((..........))))))).(((((..((....))..))))))))).-(((....((....)).....)))...------ ( -28.60, z-score =  -0.77, R)
>droAna3.scaffold_13340 4309218 85 + 23697760
------------------GGUGGCCGCAAAUUAAACGAAUUGUGGCUCGGCAUUUGGCAACAUUUGUUGCCACA-CUGACCAGUUGGGAAAGUAUCAGCAUCAU---
------------------(((((((((((.((....)).))))))))(((....(((((((....)))))))..-)))))).(((((.......))))).....--- ( -27.80, z-score =  -1.90, R)
>droWil1.scaffold_181089 3531189 96 - 12369635
GUCCACUUCUCAAUGUGCUCUAGCCACAAAUUAAACGAAUUGUGGCACAGAA-CUGGCAACAUUUGUUGCCACA-UUGACCAGAUGUAGCAACAACUG---------
.........(((((((......(((((((.((....)).)))))))......-..((((((....)))))))))-)))).(((.(((....))).)))--------- ( -29.40, z-score =  -3.27, R)
>consensus
______________U_CCGUUGGCCGCAAAUGAAACGAAUUGUGGCACAGCAUUUGGCAACAUUUGUUGCCACA_CUGACCGGCACUUGGAGCAGCAGCAU______
..................(((((((((((..........))))))).(((....(((((((....)))))))...)))..))))....................... (-18.53 = -19.40 +   0.87)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:48:09 2011